+Open data
-Basic information
Entry | Database: PDB / ID: 2cu9 | ||||||
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Title | Crystal structure of Histone chaperone cia1 | ||||||
Components | Histone chaperone cia1 | ||||||
Keywords | CHAPERONE / immunoglobulin fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information H3-H4 histone complex chaperone activity / histone chaperone activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / nucleosome assembly / chromatin organization / histone binding / chromatin remodeling / chromatin / nucleus Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Padmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal Structures of Fission Yeast Histone Chaperone Asf1 Complexed with the Hip1 B-domain or the Cac2 C Terminus Authors: Malay, A.D. / Umehara, T. / Matsubara-Malay, K. / Padmanabhan, B. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cu9.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cu9.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cu9_validation.pdf.gz | 430.8 KB | Display | wwPDB validaton report |
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Full document | 2cu9_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 2cu9_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 2cu9_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/2cu9 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/2cu9 | HTTPS FTP |
-Related structure data
Related structure data | 2z34C 2z3fC 1wg3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18347.934 Da / Num. of mol.: 1 / Fragment: N-terminal region 1-161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O74515 |
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#2: Chemical | ChemComp-PG0 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: PEG 6000, Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 17836 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.175 / Num. unique all: 1610 / % possible all: 87.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WG3 Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.947 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.102 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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